search

arq5x / lumpy-sv

lumpy: a general probabilistic framework for structural variant discovery
MIT License
307 stars 119 forks source link

deletion called by lumpy without obvious drop in depth in graph #308

Open shannjiang opened 5 years ago

shannjiang commented 5 years ago

Hi,

I used lumpy to call structural variants on my WGS data. There is one deletion detected by delly interested me and I did cnv graphs by lowresbam2raster (http://lindenb.github.io/jvarkit/LowResBam2Raster.html) to visually check it: s1329_trio1_F_DNcnv_chr13_21736017-21742126 s1329_trio1_C_DNcnv_chr13_21736017-21742126

As shown in the two cnv graphs above, both of them are from the same region, and the second sample was identified to have a deletion here by lumpy with SR (supportive reads) value equal to 10 (WGS converage for these samples is 30X). Red arch lines are those split reads. But I didn't see an obvious coverage drop of the depth in the second graph when compared to the depth of the first graph (without deletion in the region).

My question is can I still consider it as a deletion even though without obvious drop in depth for the second graph? Attached please find the result by delly for the second sample. s1329_trio1_child_lumpy.txt

thanks,

Shan

ryanlayer commented 5 years ago

I would be a bit suspect if there is no drop in coverage. Does it overlap a repetitive region?

On Jul 2, 2019, at 11:53 AM, shannjiang notifications@github.com wrote:

Hi,

I used lumpy to call structural variants on my WGS data. There is one deletion detected by delly interested me and I did cnv graphs by lowresbam2raster (http://lindenb.github.io/jvarkit/LowResBam2Raster.html) to visually check it:

As shown in the two cnv graphs above, both of them are from the same region, and the second sample was identified to have a deletion here by lumpy with SR (supportive reads) value equal to 10 (WGS converage for these samples is 30X). But I didn't see an obvious coverage drop of the depth in the second graph when compared to the depth of the first graph (without deletion in the region).

My question is can I still consider it as a deletion even though without obvious drop in depth for the second graph? Attached please find the result by delly for the second sample. s1329_trio1_child_lumpy.txt

thanks,

Shan

— You are receiving this because you are subscribed to this thread. Reply to this email directly, view it on GitHub, or mute the thread.